I am looking at a Mainship 35 foot, which only steers from the up stairs. Is this a concern? Do folks seem to feel that it can get too hot or buggy? The Mainship 40 foot gives me both options of driving from the top or bottom, do most find this a better option?

I don't use the FB helm much. Unless its quite warm the wind chill up there takes away the enjoyment a bit. Plus, I much prefer the nav displays in the raised pilothouse.

If the FB is your only helm you would need clears to give you all-weather capability. But there is not much else to like about clears. Having said that, I would not let that aspect be anything other than a minor factor in choosing the boat. You can make it work, there is something to be said about only having one helm and sets of controls and nav stuff.

I'm guessing you will get answers all over the place.
Some will only have bridge helms...Others have both and will never use lower... I'd say it depends on your style and area of boating.
Are you comfortable in rough conditions from upper?
Do you have hard windshield & wipers on upper?...Will you ever want to operate in rain or only fair weather?
How !Any aboard to help w locking& docking...Will you ever need /want to single hand locking, docking or rafting?
Do you and crew like to climb ladders / stairs or keep comfortable on one level.
Fly brides can be wonderful on nice days...Even when in Port or at anchor.
Lower helms can be comfortable in less than ideal conditions.
No one right answer... That's why you find different designs.
You have the consider what will work best for you & our crew.

Many dual-helm boats have pretty bad visibility from the lower helm which is another concern. I like driving downstairs especially if it's cold and wet. In good weather, though, it's tough to beat driving from the flybridge.

When we lived in SoCal and our typical trip was from Long Beach to Catalina Island, we used the flybridge on our Mainship 34T almost exclusively. Only when the seas got up to 5' or beyond did we go below to limit the roll acceleration that you get up on the fly bridge in those conditions.

Now that we boat in New England our downeast style Mainship Pilot 34 works great and only on some of the hot days in the mid summer do we miss a fly bridge.

We have an H-38. We boat from New England to the Keys. The pilothouse visibility is excellent. It is actually cooler on a hot day than up on the bridge. Less sun, less wind, more comfort and we like the electronics displays. It give us much better access to docking lines and lock lines. 2800 engine hours in 9 seasons and less than 10 hours driving from the bridge. But the bridge is a great place to entertain and have a glass of wine while watching the sun set.

When we lived in SoCal and our typical trip was from Long Beach to Catalina Island, we used the flybridge on our Mainship 34T almost exclusively.

Our boat only has a helm on the flybridge. We looked for that specifically when our search was in progress. In place of the down helm is our dinette which we use all the time. As David posted above, in SoCal, a flybridge helm sure is nice!

My pre-trawler days were spent in the open on sailboats. Enough of that! I now stay in the trawler's pilothouse and avoid paying extra for a flybridge. (If buying a used boat, the most common boat is white, have twin engines, and a flybridge.) I'd avoid a boat which can only be controlled from a flybridge.

My pilothouse has less motion than a flybridge, more convenient for dock-handling, and is more protective from hostile environmental factors (sun, wind, extreme temperatures).

I would say a lot depends on the area you cruise and whether you have visibility from the lower helm like Scott stated. I had a 46 Hatt that had zero visibility from the lower station so the windows got painted and covered. Our 34 and now our current boat has both upper and lower helms but the are only used in really bad weather which is probably two tines a year in South Florida. We boat a lot in the Bahamas and need to read the water, I also like the breeze and smells on the bridge. Our hard top extends pretty far forward so rain gear is seldom needed.

We have a Mainship 390 with upper and lower and drive mostly from the flybridge. From your nomenclature (35 & 40) and description I think you're talking about the 35' convertible and the 40' Nantucket. If so, these are very different boats as the Nantucket has an aft cabin. From your area I would suspect you would drive mostly from the flybridge so maybe you should also look at the rest of the boat to see which fits your needs.
Mainship also made 350/390 and 400 trawlers that have upper and lower stations.
John

I love steering from the FB, but when it's cool and rainy and we still want to move on to the next spot, it's sure nice to be able to operate from below, with the heater on, some tunes and coffee. Both is best. But we are in Canada and even in summer it can go from hot and muggy to cold and rainy the next day.

We have both, but mostly drive from the lower helm. Up top everything you want is down below, be it food, drink, sunglasses, the local chart, etc. But maybe even more importantly, and aside from the boat handling, docking, access issues others have raised, especially if like me ones other half is not as keen, and loves to read when out, it can get pretty lonely being the only one up there because you're driving.

Not a lot of folk who aren't mad keen like to just sit up there keeping the skipper company. If you're both downstairs, you can at least exchange comments, draw attention to a passing things of interest, and discuss proposed routes, anchorages, and when and what you'd like for a drink, meal, whatever. I would never buy a boat without a lower inside helm. I guess a pilothouse set-up is the best compromise all round.

I think the difference is in the length of the passage. When we took our first boat (sedan set up w/ flybridge) down the ICW I used the lower stations exclusively. We now have a pilot house w/ flybridge. Still use lower station exclusively. A few hours with the wind, noise, sun, etc. becomes fatiguing. Offshore, forget any upper helm except maybe the perfect trip to Bahamas, again 60-70-90 hrs offshore forget it.

So depends on your type of cruising. Short trips = great. Entertaining =great.